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PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z31792168
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 15% PEG 4K, 5% DMSO
Crystal Properties Matthews coefficient Solvent content 1.93 36.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.146 α = 90 b = 53.167 β = 101.66 c = 44.267 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2020-02-27 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9126 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.83 55.4 99.7 0.14 0.164 0.084 0.995 5.6 3.7 22904
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.93 99.8 1.619 1.878 0.941 0.455 3.8 3333
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6LU7 1.83 55.4 21632 1152 99.04 0.2205 0.2167 0.248 0.2926 0.2867 RANDOM 38.925
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.57 2.78 -2.47 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.627 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_4_deg 13.273 r_dihedral_angle_1_deg 7.892 r_mcangle_it 3.562 r_mcbond_other 2.154 r_mcbond_it 1.899 r_angle_refined_deg 1.412 r_angle_other_deg 1.256 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.627 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_4_deg 13.273 r_dihedral_angle_1_deg 7.892 r_mcangle_it 3.562 r_mcbond_other 2.154 r_mcbond_it 1.899 r_angle_refined_deg 1.412 r_angle_other_deg 1.256 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing